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Abstract

This paper describes conformational transitions of flexible biomolecules, especially
proteins. Molecules tend to naturally occur in stable (or minimum energy)
conformations. Dynamics methods can be used to model a molecule through use of
computer simulation. Within a generated trajectory, we expect the molecule to exist
and make transitions between minimum energy conformations. High activation energy
barriers prevent frequent transitions. Generalized density dynamics techniques
will be utilized to increase the sampling of molecules in different stable molecular
conformations. Paths within the trajectory that contain transitions can then be
isolated. Once isolated, a transitional trajectory can be optimized to a minimum
energy path (MEP) between two minimum energy conformations. The MEP will
help discover the activation energy of the molecule according to the min-max principle
(taking the lowest path over a barrier). The CHARMM package, along with
MATLAB and gOpenMol, will be used to analyze the physical conformations of
alanine dipeptide (as a test case). Further, we describe work on larger helical model
protein systems.